RetrogeneDB ID: retro_amel_855

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192683.1:1015145..1015986(-)
• Located in intron of: ENSAMEG00000009899

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000016077
• Aliases: None
• Description: None

Sequence

>retro_amel_855
GTGGCAGCCATGAAGATCCTGAATGCCAAGGCCAAGGTAGCCCAAGCCCAGGAGGCACTGGCAGTTAACATCAGTGTGGC
CCAGGGGCTGCAGGACATGCTGAGGACCAACTTGGGGCCTAAGGGCACTGTGAAGATGTTTGTTCTGGTACTGGAGACAT
CAAACTTACTGAAGATGGCAATGTGCTGCCTCATGAAATGCAAATTCAACACCCAACAGCCTCCTTAATAGCCAAAGTGG
CAACAGCCCAGGATGACATAACTGGTGATGGTACCACTTCCAATGTCTTAAAAACTGGAGAGCTACTGAAACAGGTGGAT
CTCTACATTTCTGAAGGTCTTCATTCCAGTATAACAACAGAAGGACTTGAGGCTACAAAGGAAAAGGCACTCCAGTTTTT
GAAACAAGTCAAAGTAAGCAGAGAAATGGACAGGGAAGCACTTATAAATGTGGCCAGAACATCTCTACCTCCTAAAGTAC
ATGCTGAATTTGCTGATGTCTTAACAGAGGCTGTAGTGGACTCCATTTTGGTCATTAAAAAACAAGCTGAACCTACTGAA
CTCTTCATGTTTGAGATCATGGAAATGAAACAGAAATCTGAAACTGATAAAAGCTTAATCAGAAGTCTTGCTTTGGACCA
TGGGGTGCACATCCTGGTATGAAAAGAAAAAAAGAAGATGCATACATCCTCACGTGCAGTGTGTCATTAGAATATGAAAA
AACAAGTGAATTCTGGCTTTTCTTTACAAGAGTTCAGAAGGAGGAGAGAAACTTGTAAAAGCTGAAAGAAAATTCATTGA
AGATAGAGTTAAAAAATAATAGAACTGAAAAAGAAAGTCTG

Alignment

ORF - retro_amel_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 52.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAAVKTLNPKAEVARAQAALAVNISAARGLQDVLRTNLGPKGTMKMLV-SGAGDIKLTKDGNVLLHEMQI
          .AA.K.LN.KA.VA.AQ.ALAVNIS.A.GLQD.LRTNLGPKGT.KM.V.SG.GDIKLT.DGNVL.HEMQI
Retrocopy VAAMKILNAKAKVAQAQEALAVNISVAQGLQDMLRTNLGPKGTVKMFV<SGTGDIKLTEDGNVLPHEMQI

Parental  QHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEGLHPRIITEGFEAAKEKALQFLEQVKV
          QHPTASLIAKVATAQDDITGDGTTSNVL..GELLKQ.DLYISEGLH..I.TEG.EA.KEKALQFL.QVKV
Retrocopy QHPTASLIAKVATAQDDITGDGTTSNVLKTGELLKQVDLYISEGLHSSITTEGLEATKEKALQFLKQVKV

Parental  SKEMDRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKQDEPIDLFMVEIMEMKHKSETDTSLIRG
          S.EMDRE.LI.VARTSL..KVHAE.ADVLTEAVVDSIL.IKKQ.EP..LFM.EIMEMK.KSETD.SLIR.
Retrocopy SREMDREALINVARTSLPPKVHAEFADVLTEAVVDSILVIKKQAEPTELFMFEIMEMKQKSETDKSLIRS

Parental  LVLDHGAR-HPDMKKRVEDAYILTCNVSLEYEKTEVNSGFF-YKSAEEREKLVKAER-NSLK-QLK-KRT
          L.LDHG...HP.MK...EDAYILTC.VSLEYEKT.....FF.YKS.E..EKLVKAER.NSLK..LK..RT
Retrocopy LALDHGVH<HPGMKRKKEDAYILTCSVSLEYEKTSEFWLFF<YKSSEGGEKLVKAER>NSLKIELKNNRT

Parental  EKGSL
          EK.SL
Retrocopy EKESL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_855 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_855 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016077	1 retrocopy	retro_amel_855 ,
Canis familiaris	ENSCAFG00000010149	1 retrocopy	retro_cfam_431,
Choloepus hoffmanni	ENSCHOG00000000654	3 retrocopies	retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus	ENSCJAG00000021279	2 retrocopies	retro_cjac_1320, retro_cjac_580,
Dipodomys ordii	ENSDORG00000001249	1 retrocopy	retro_dord_617,
Felis catus	ENSFCAG00000027654	2 retrocopies	retro_fcat_1102, retro_fcat_320,
Homo sapiens	ENSG00000146731	2 retrocopies	retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla	ENSGGOG00000011439	1 retrocopy	retro_ggor_133,
Loxodonta africana	ENSLAFG00000012791	1 retrocopy	retro_lafr_808,
Macaca mulatta	ENSMMUG00000015272	1 retrocopy	retro_mmul_2582,
Monodelphis domestica	ENSMODG00000006565	1 retrocopy	retro_mdom_1330,
Nomascus leucogenys	ENSNLEG00000015664	1 retrocopy	retro_nleu_1355,
Oryctolagus cuniculus	ENSOCUG00000017674	1 retrocopy	retro_ocun_468,
Procavia capensis	ENSPCAG00000015532	1 retrocopy	retro_pcap_263,
Pongo abelii	ENSPPYG00000025820	1 retrocopy	retro_pabe_2719,
Pan troglodytes	ENSPTRG00000019206	2 retrocopies	retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus	ENSPVAG00000001421	1 retrocopy	retro_pvam_663,
Rattus norvegicus	ENSRNOG00000000923	1 retrocopy	retro_rnor_2226,